:: DESCRIPTION
CKSAAP-Palm (composition of k-spaced amino acid pairs ) is a tool for predicting palmitoylation sites based on protein sequence.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Xiao-Bo Wang, Ling-Yun Wu, Yong-Cui Wang, and Nai-Yang Deng.
Prediction of palmitoylation sites using the composition of K-spaced amino acid pairs.
Protein Engineering, Design and Selection (2009) 22 (11): 707-712.
:: DESCRIPTION
PROTARCH package uses a united-residue representation of the polypeptide chain and the Conformational Space Annealing search method to predict a protein structure. The key stage of the method is global optimization of the energy of a polypeptide chain at the simplified united-residue level. PROTARCH also includes computational tools to carry out cluster analysis and construction of all-atom backbone from the united-residue chain using the dipole-path method.
::DEVELOPER
Computational Biology Service Unit
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Philius predicts protein transmembrane topology and signal peptides.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Transmembrane topology and signal peptide prediction using dynamic Bayesian networks
Sheila M. Reynolds, Lukas K?ll, Michael E. Riffle, Jeff A. Bilmes and William Stafford Noble
PLoS Computational Biology. 4(11):e1000213, 2008.
:: DESCRIPTION
RNAmotifs allows you to predict a structural motif common to a set of RNA sequences. The resulting motifs includes information on both RNA sequence and structure. Motifs are described both graphically and by a data file containing information on the underlying probabilistic model.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rabani et. al,
Computational prediction of RNA structural motifs involved in post transcriptional regulatory processes,
Proc Natl Acad Sci U S A., September 2008
:: DESCRIPTION
PrediSi (PREDIction of SIgnal peptides) is a software tool for predicting signal peptide sequences and their cleavage positions in bacterial and eukaryotic proteins.It is especially useful for the fast analysis of large datasets because calculation is performed in real time with a high accuracy. Therefore PrediSi is well suited for the evaluation of whole proteome datasets which are currently accumulating during numerous genome projects and proteomics experiments.
::DEVELOPER
Karsten Hiller (k.hiller@tu-bs.de) @ Institute for Microbiology, Technical University of Braunschweig
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Hiller, K., Schobert, M., Hundertmark, C., Jahn, D. & Münch, R. (2003)
JVirGel: calculation of virtual two-dimensional protein gels.
Nucleic Acids Res. 31, 3862-3865
:: DESCRIPTION
RNAstrand predicts the reading direction of a structured RNA gene from a multiple sequence alignment and its reverse complement. It is meant as a post processing tool for RNA prediction tools which in general do not reliable annotate the reading direction of the structured RNA candidate.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
RNAstrand: Reading direction of structured RNAs in multiple sequence alignments
Kristin Reiche, Peter F. Stadler,
Algorithms for Molecular Biology, 2:6, 2007.
:: DESCRIPTION
The HotKnots program predicts secondary structures of RNA molecules with or without pseudoknots.
::DEVELOPER
BETA LAB – University of British Columbia
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Ren, J., Rastegari, B., Condon, A., and Hoos, H. H. (2005).
HotKnots: heuristic prediction of RNA secondary structures including pseudoknots.
RNA, 11(10), 1494–1504.
:: DESCRIPTION
IRECS ( REduction of Conformational Space) can predict multiple conformations for all side chains of a target protein. Side-chain conformations are selected according to the flexibility of the respective side chain. IRECS is also able to mutate single side chains or read in alignments to create a homology model of the target protein on a template backbone.
::DEVELOPER
Max-Planck-Institut Informatik
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Hartmann, C., Antes, I., Lengauer, T.
IRECS: A new algorithm for the selection of most probable ensembles of side-chain conformations in protein models.
Protein Sci. 2007 16: 1294-1307.
:: DESCRIPTION
IUPred is a web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content.Prediction of Intrinsically Unstructured Proteins. Intrinsically unstructured / disordered proteins have no single well-defined tertiary structure in their native, functional state. Our server recognizes such regions from the amino acid sequence based on the estimated pairwise energy content.
DEVELOPER
Institute of Enzymology,the Biological Research Center of the Hungarian Academy of Sciences.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
Zsuzsanna Dosztányi, Veronika Csizmók, Péter Tompa and István Simon
Bioinformatics (2005) 21, 3433-3434.
:: DESCRIPTION
ANCHOR aims to predict binding regions in proteins that are disordered in isolation but can undergo a disorder-to-order transition upon binding to a structured protein partner. The approach is based on the energy estimation method and it uses a single amino acid sequence as an input.
DEVELOPER
Institute of Enzymology,the Biological Research Center of the Hungarian Academy of Sciences.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Zsuzsanna Dosztányi, Bálint Mészáros and István Simon (2009)
ANCHOR: web server for predicting protein binding regions in disordered proteins
Bioinformatics 25(20): 2745-2746.
